I have tried reinstalling and dpkg-reconfigureing both command-not-found{,-data} but these don't seem to have fixed it. Is it safe to delete these files, or do I have to run some program to recreate them? I should add that this was originally a 32-bit install that I reinstalled with 64-bit without formatting the disk.

1 Answer
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The database files for the 64 bit version are named amd64-*.db, while the 32 bit version ones are named i386-*.db. So apparently you have the 32 bit package installed when you should've had the 64 bit package.

@dutchie, hm. Does this list both amd64-*.db and i386-*.db files? ls /usr/share/command-not-found/programs.d/. If so, it might be the old package just failed to remove those for some reason. So just manually removing them should fix your problem.
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geirhaJul 25 '13 at 18:02